{"id":"https://openalex.org/W4285088295","doi":"https://doi.org/10.1371/journal.pcbi.1010322","title":"Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models","display_name":"Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models","publication_year":2022,"publication_date":"2022-07-13","ids":{"openalex":"https://openalex.org/W4285088295","doi":"https://doi.org/10.1371/journal.pcbi.1010322","pmid":"https://pubmed.ncbi.nlm.nih.gov/35830470"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010322","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010322","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010322&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010322&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003197068","display_name":"Fabian Fr\u00f6hlich","orcid":"https://orcid.org/0000-0002-5360-4292"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fabian Fr\u00f6hlich","raw_affiliation_strings":["Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-5360-4292","affiliations":[{"raw_affiliation_string":"Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063426870","display_name":"Peter K. Sorger","orcid":"https://orcid.org/0000-0002-3364-1838"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter K. Sorger","raw_affiliation_strings":["Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3364-1838","affiliations":[{"raw_affiliation_string":"Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5003197068","https://openalex.org/A5063426870"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210155419"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.1247,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.92922844,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"18","issue":"7","first_page":"e1010322","last_page":"e1010322"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10848","display_name":"Advanced Multi-Objective Optimization Algorithms","score":0.9879000186920166,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hessian-matrix","display_name":"Hessian matrix","score":0.7346303462982178},{"id":"https://openalex.org/keywords/ode","display_name":"Ode","score":0.692404568195343},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6381788849830627},{"id":"https://openalex.org/keywords/ordinary-differential-equation","display_name":"Ordinary differential equation","score":0.5134633183479309},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.490405797958374},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.4165901243686676},{"id":"https://openalex.org/keywords/calibration","display_name":"Calibration","score":0.41415935754776},{"id":"https://openalex.org/keywords/identifiability","display_name":"Identifiability","score":0.4107147455215454},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3942476511001587},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3777473270893097},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37085357308387756},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.27427810430526733},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2682250440120697},{"id":"https://openalex.org/keywords/differential-equation","display_name":"Differential equation","score":0.2468550205230713},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.106610506772995}],"concepts":[{"id":"https://openalex.org/C203616005","wikidata":"https://www.wikidata.org/wiki/Q620495","display_name":"Hessian matrix","level":2,"score":0.7346303462982178},{"id":"https://openalex.org/C34862557","wikidata":"https://www.wikidata.org/wiki/Q178985","display_name":"Ode","level":2,"score":0.692404568195343},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6381788849830627},{"id":"https://openalex.org/C51544822","wikidata":"https://www.wikidata.org/wiki/Q465274","display_name":"Ordinary differential equation","level":3,"score":0.5134633183479309},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.490405797958374},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.4165901243686676},{"id":"https://openalex.org/C165838908","wikidata":"https://www.wikidata.org/wiki/Q736777","display_name":"Calibration","level":2,"score":0.41415935754776},{"id":"https://openalex.org/C122770356","wikidata":"https://www.wikidata.org/wiki/Q1656753","display_name":"Identifiability","level":2,"score":0.4107147455215454},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3942476511001587},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3777473270893097},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37085357308387756},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.27427810430526733},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2682250440120697},{"id":"https://openalex.org/C78045399","wikidata":"https://www.wikidata.org/wiki/Q11214","display_name":"Differential equation","level":2,"score":0.2468550205230713},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.106610506772995},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035502","descriptor_name":"Trust","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035502","descriptor_name":"Trust","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035502","descriptor_name":"Trust","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035502","descriptor_name":"Trust","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1010322","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010322","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010322&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:35830470","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35830470","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1010322","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010322","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:1abfb8fed9474178beeccef7b01e22c6","is_oa":true,"landing_page_url":"https://doaj.org/article/1abfb8fed9474178beeccef7b01e22c6","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 7, p e1010322 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9312381","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9312381","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010322","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010322","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010322&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2257353674","display_name":null,"funder_award_id":"LT000259/2019-L1","funder_id":"https://openalex.org/F4320307846","funder_display_name":"Human Frontier Science Program"},{"id":"https://openalex.org/G5612980095","display_name":null,"funder_award_id":"U54-CA225088","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320307846","display_name":"Human Frontier Science Program","ror":"https://ror.org/02ebx7v45"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4285088295.pdf","grobid_xml":"https://content.openalex.org/works/W4285088295.grobid-xml"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W1968553199","https://openalex.org/W1975444080","https://openalex.org/W1985911638","https://openalex.org/W1986224264","https://openalex.org/W1989151663","https://openalex.org/W2005136695","https://openalex.org/W2009435671","https://openalex.org/W2018624971","https://openalex.org/W2038210983","https://openalex.org/W2038742368","https://openalex.org/W2053874495","https://openalex.org/W2053964895","https://openalex.org/W2057565823","https://openalex.org/W2057667075","https://openalex.org/W2067251243","https://openalex.org/W2071467620","https://openalex.org/W2078409719","https://openalex.org/W2085137170","https://openalex.org/W2087752119","https://openalex.org/W2102434872","https://openalex.org/W2103111465","https://openalex.org/W2109571753","https://openalex.org/W2118040915","https://openalex.org/W2119842211","https://openalex.org/W2122825283","https://openalex.org/W2143784594","https://openalex.org/W2146989110","https://openalex.org/W2151554678","https://openalex.org/W2161304688","https://openalex.org/W2166751342","https://openalex.org/W2168648059","https://openalex.org/W2179083909","https://openalex.org/W2236623899","https://openalex.org/W2507812261","https://openalex.org/W2569195183","https://openalex.org/W2741052609","https://openalex.org/W2800980964","https://openalex.org/W2808342221","https://openalex.org/W2808626003","https://openalex.org/W2891577962","https://openalex.org/W2902000707","https://openalex.org/W2949499968","https://openalex.org/W2950665010","https://openalex.org/W2952056515","https://openalex.org/W2963586744","https://openalex.org/W2964392985","https://openalex.org/W2980134341","https://openalex.org/W2994954405","https://openalex.org/W3003257820","https://openalex.org/W3014365047","https://openalex.org/W3024659207","https://openalex.org/W3035965352","https://openalex.org/W3099878876","https://openalex.org/W3103145119","https://openalex.org/W3107157582","https://openalex.org/W3142344196","https://openalex.org/W4213032059","https://openalex.org/W4238726034","https://openalex.org/W4301014524","https://openalex.org/W4318167261"],"related_works":["https://openalex.org/W3215072370","https://openalex.org/W2113105229","https://openalex.org/W3082668976","https://openalex.org/W2517973022","https://openalex.org/W1543121148","https://openalex.org/W1580703421","https://openalex.org/W2618518959","https://openalex.org/W2231364979","https://openalex.org/W4295745414","https://openalex.org/W3161724164"],"abstract_inverted_index":{"Ordinary":[0],"differential":[1],"equation":[2],"(ODE)":[3],"models":[4,33,53,263],"are":[5,34,82,97,162],"widely":[6,193],"used":[7,194],"to":[8,67,126,133,224,252,265],"study":[9],"biochemical":[10,70,262],"reactions":[11],"in":[12,169,191,261],"cellular":[13],"networks":[14,24],"since":[15],"they":[16],"effectively":[17],"describe":[18],"the":[19,176,192,225],"temporal":[20],"evolution":[21],"of":[22,31,51,77,130,140,152,175,182,185,227,247],"these":[23,32,88,204],"using":[25,46,244],"mass":[26],"action":[27],"kinetics.":[28],"The":[29],"parameters":[30],"rarely":[35],"known":[36],"a":[37,121,138,148,207,245,267],"priori":[38],"and":[39,111,197,217,239,264],"must":[40],"instead":[41],"be":[42,253,266],"estimated":[43],"by":[44],"calibration":[45,50,72,103,136],"experimental":[47,160],"data.":[48],"Optimization-based":[49],"ODE":[52,134,257],"on":[54,147,235],"is":[55,73,104],"often":[56],"challenging,":[57,74],"even":[58],"for":[59,93,106,157,256,269],"low-dimensional":[60],"problems.":[61],"Multiple":[62],"hypotheses":[63],"have":[64],"been":[65],"advanced":[66],"explain":[68],"why":[69],"model":[71,78,102,109,135],"including":[75],"non-identifiability":[76],"parameters,":[79],"but":[80],"there":[81],"few":[83],"comprehensive":[84],"studies":[85,96],"that":[86,213,232],"test":[87,228],"hypotheses,":[89],"likely":[90],"because":[91],"tools":[92],"performing":[94],"such":[95],"also":[98],"lacking.":[99],"Nonetheless,":[100],"reliable":[101,238],"essential":[105],"uncertainty":[107],"analysis,":[108],"comparison,":[110],"biological":[112],"interpretation.":[113],"We":[114,144,202,249],"implemented":[115],"an":[116],"established":[117],"trust-region":[118],"method":[119],"as":[120],"modular":[122],"Python":[123],"framework":[124],"(fides)":[125],"enable":[127],"systematic":[128],"comparison":[129],"different":[131,173],"approaches":[132],"involving":[137],"variety":[139,246],"Hessian":[141,199,210],"approximation":[142,200,211],"schemes.":[143,201],"evaluated":[145],"fides":[146,233,251],"recently":[149],"developed":[150],"corpus":[151,226],"biologically":[153],"realistic":[154],"benchmark":[155],"problems":[156,260],"which":[158],"real":[159],"data":[161],"available.":[163],"Unexpectedly,":[164],"we":[165,230],"observed":[166],"high":[167],"variability":[168],"optimizer":[170,187,215],"performance":[171,188,216],"among":[172],"implementations":[174],"same":[177],"mathematical":[178],"instructions":[179],"(algorithms).":[180],"Analysis":[181],"possible":[183],"sources":[184],"poor":[186],"identified":[189],"limitations":[190],"Gauss-Newton,":[195],"BFGS":[196],"SR1":[198],"addressed":[203],"drawbacks":[205],"with":[206],"novel":[208],"hybrid":[209,220],"scheme":[212],"enhances":[214],"outperforms":[218],"existing":[219,242],"approaches.":[221],"When":[222],"applied":[223],"models,":[229],"found":[231],"was":[234],"average":[236],"more":[237],"efficient":[240],"than":[241],"methods":[243,271],"criteria.":[248],"expect":[250],"broadly":[254],"useful":[255],"constrained":[258],"optimization":[259],"foundation":[268],"future":[270],"development.":[272]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
